Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate GFF2666 Psest_2719 acetylornithine and succinylornithine aminotransferases/succinylornithine transaminase family
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__psRCH2:GFF2666 Length = 406 Score = 196 bits (497), Expect = 1e-54 Identities = 138/405 (34%), Positives = 205/405 (50%), Gaps = 42/405 (10%) Query: 21 GRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLAL 80 G + VWD G+ +DF GGI V LGH +PA+V A+ QA +L H + N + P L L Sbjct: 31 GLGSRVWDQSGRELVDFAGGIAVNALGHAHPAMVAALTEQAGKLWHIS-NIYTNEPALRL 89 Query: 81 MEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG------ATGKRAIIAFDGGFHGRTL 134 ++L V ++ NSGAEA E A K+AR K II+ FHGRTL Sbjct: 90 AKKL---VAATFADRAFFCNSGAEANEAAFKLARRYAHDVYGPQKFEIISALNSFHGRTL 146 Query: 135 ATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVED-VAA 193 T+ + G+ + Y G + H+PY + ALKA A+ D A Sbjct: 147 FTVTVGGQ-SKYSDGFGPKIEGITHVPYNDLE-------ALKA---------AISDKTCA 189 Query: 194 FIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPD 253 + EP+QGE G L + A+ + R+ C+E L+I DE+Q+G GRTG+ FA+ GI PD Sbjct: 190 VVLEPIQGESGILPGEQAYLEGARQLCNEHNALLIFDEVQTGMGRTGELFAYMHYGITPD 249 Query: 254 LLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLAT 313 +L AKS+ GG P+GA++ E+ A L G G TY GNP++CA A A + + + Sbjct: 250 ILTNAKSLGGGFPIGAMLTTNEIAAHLSVGTHGTTYGGNPLACAVAEAVVDIVNTPEVL- 308 Query: 314 WGERQEQAIVSRYERWKASGLSPYIGRLTGVGAM---RGIEFANADGSPAPAQLAKVMEA 370 + + +++ER+KA IG GV ++ RG+ + A Sbjct: 309 ------EGVKAKHERFKAR--LTQIGERYGVFSLVRGRGLLIGCVLSDAWKGKAGAFCAA 360 Query: 371 ARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 A L+++ +G ++RL L I+ ++EGLD LE+ +A L Sbjct: 361 AEKEALMVLQAGP--DVVRLAPSLVIDQADIDEGLDRLERAVAAL 403 Lambda K H 0.320 0.137 0.402 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 450 Number of extensions: 20 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 416 Length of database: 406 Length adjustment: 31 Effective length of query: 385 Effective length of database: 375 Effective search space: 144375 Effective search space used: 144375 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory